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Test ID COGBF B-Lymphoblastic Leukemia/Lymphoma, Children’s Oncology Group Enrollment Testing, FISH, Varies


Advisory Information


This test is only performed on specimens from pediatric patients being considered for enrollment in a Children's Oncology Group (COG) protocol. For all other patients, order BALLF / B-Lymphoblastic Leukemia/Lymphoma, FISH, Varies.



Shipping Instructions


Advise Express Mail or equivalent if not on courier service.



Necessary Information


1. Provide a reason for referral with each specimen, as well as flow cytometry and/or a bone marrow pathology report and a Children’s Oncology Group (COG) protocol number. The laboratory will not reject testing if this information is not provided, but appropriate testing and interpretation may be compromised or delayed.

2. If a child has received an opposite sex bone marrow transplant prior to specimen collection for this protocol, convey this information to the laboratory.



Specimen Required


Submit only 1 of the following specimens:

 

Preferred:

Specimen Type: Bone marrow
Container/Tube: Green top (sodium heparin)
Specimen Volume: 1 to 2 mL
Collection Instructions: Invert several times to mix bone marrow.

Acceptable:

Specimen Type: Blood
Container/Tube: Green top (sodium heparin)
Specimen Volume: 6 mL
Collection Instructions: Invert several times to mix blood.


Useful For

Evaluation of pediatric bone marrow and peripheral blood specimens by FISH probe analysis for classic rearrangements and chromosomal copy number changes associated with B lymphoblastic leukemia/lymphoma and Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) in patients being considered for enrollment in Children's Oncology Group (COG) clinical trials and research protocols

 

As an adjunct to conventional chromosome studies in performed in pediatric patients with B-ALL and Ph-like ALL being considered for enrollment in COG protocols

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
_PBCT Probe, +2 No, (Bill Only) No
_PADD Probe, +1 No, (Bill Only) No
_PB02 Probe, +2 No, (Bill Only) No
_PB03 Probe, +3 No, (Bill Only) No
_IL25 Interphases, <25 No, (Bill Only) No
_I099 Interphases, 25-99 No, (Bill Only) No
_I300 Interphases, >=100 No, (Bill Only) No

Testing Algorithm

This test is only performed on specimens from pediatric patients who are candidates for enrollment in Children's Oncology Group (COG) clinical trials and research protocols and may be ordered in 4 distinct ways allowing different combinations of probes to be utilized based on the clinical question:

-Standard (diagnostic) B-lymphoblastic leukemia/lymphoma (B-ALL) FISH panel

-Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) panel

-Combined-Standard (diagnostic) B-ALL FISH panel + Ph-like ALL panel

-Individual B-ALL FISH probes (per client request)

 

The specific B-ALL FISH panel or FISH probes requested must be noted on the request form or in the reason for referral. If no specific panel or FISH probe request is indicated, the "Standard (diagnostic) B-ALL FISH panel" will be performed.

 

The Standard (diagnostic) B-ALL FISH panel includes testing for the following abnormalities, using the FISH probes listed:

Hyperdiploidy, +4,+10,+17: D4Z1/D10Z1/D17Z1

t(12;21)(p13;q22), ETV6/RUNX1 fusion, ETV6/RUNX1 D-FISH

iAMP21, RUNX1 amplification, ETV6/RUNX1 D-FISH

t(9;22)(q34;q11.2), BCR/ABL1 fusion, BCR/ABL1 D-FISH

t(1;19)(q23;p13), PBX1/TCF3 fusion, PBX1/TCF3 D-FISH

t(11q23;var), MLL (KMT2A) rearrangement, MLL (KMT2A) break-apart

del(9p), CDKN2A deletions, CDKN2A/D9Z1

t(14q32;var), IGH rearrangement, IGH break-apart

del(17p), TP53 deletions, TP53/D17Z1

8q24.1 rearrangement, MYC break-apart

t(Xp22.33;var) or t(Yp11.32;var), P2RY8 rearrangement, P2RY8 break-apart

t(Xp22.33;var) or t(Yp11.32;var), CRLF2 rearrangement, CRLF2 break-apart

 

-When an MLL (KMT2A) rearrangement is identified, reflex testing will be performed to identify the translocation partner. Probes include identification of t(4;11)(q21;q23) AFF1/MLL, t(6;11)(q27;q23) MLLT4/MLL, t(9;11)(p22;q23) MLLT3/MLL, t(10;11)(p13;q23) MLLT10/MLL, t(11;19)(q23;p13.1) MLL/ELL, or t(11;19)(q23;p13.3) MLL/MLLT1.

-When an IGH and/or CRLF2 rearrangement is identified, reflex testing will be performed using the CRLF2/IGH fusion probe set to identify a potential t(X;14)(p22.33;q32) or t(Y;14) (p11.32;q32) cryptic translocation.

-When an extra signal of ABL1 is identified in BCR/ABL1 testing, reflex testing will be performed using the ABL1 break-apart probe set to identify the presence or absence of an ABL1 rearrangement.

-If a MYC rearrangement is identified, break-apart probe sets for BCL2 and BCL6 may be performed.

 

*The "Standard (diagnostic) B-ALL FISH panel" will be automatically reflexed to the Philadelphia Ph-like ALL panel on pediatric and young adult patients (age <30) who demonstrate normal or nonclassical abnormalities on the Standard (diagnostic) panel. In other circumstances, the Ph-like ALL panel may be recommended and the client notified before performing this testing.

 

The Ph-like ALL panel includes testing for the following kinase activating chromosome abnormalities, using the FISH probes listed below as well as IKZF1 deletion which often accompanies Ph-like ALL:

-t(1q25;var), ABL2 rearrangement, ABL2 break-apart

-t(5q33;var), PDGFRB rearrangement, PDGFRB break-apart

-t(9p24.1;var), JAK2 rearrangement, JAK2 break-apart

-t(9q34;var), ABL1 rearrangement, ABL1 break-apart

-t(Xp22.33;var) or t(Yp11.32;var), P2RY8 rearrangement, P2RY8 break-apart

-t(Xp22.33;var) or t(Yp11.32;var), CRLF2 rearrangement, CRLF2 break-apart

 

-When a PDGFRB rearrangement is identified, reflex testing will be performed using the PDGFRB/ETV6 fusion probe set to identify the potential t(5;12)(q33;p13) translocation.

-When a CRLF2 rearrangement is identified, reflex testing will be performed using the CRLF2/IGH fusion probe set to identify a potential t(X;14)(p22.33;q32) or t(Y;14) (p11.32;q32) "cryptic translocation."

 

This test includes a charge for application of the first probe set (2 FISH probes) and professional interpretation of results. Additional charges will be incurred for all reflex probes performed. Analysis charges will be incurred based on the number of cells analyzed per probe set. If no cells are available for analysis, no analysis charges will be incurred.

 

The following testing algorithm is recommended for patients with B-lymphoblastic leukemia/lymphoma (B-ALL):

-At diagnosis, standard (diagnostic) B-ALL FISH panel and/or conventional chromosome studies (COGBM / Chromosome Analysis, Hematologic Disorders, Children's Oncology Group Enrollment Testing, Bone Marrow) should be performed. If there is limited specimen available, only the COGBF / B-Lymphoblastic Leukemia/Lymphoma, Children's Oncology Group Enrollment Testing, FISH, Varies will be performed.

-For children in whom disease relapse or a secondary myeloid neoplasm is a concern and enrollment in a new COG protocol is being considered; COGBM for bone marrow chromosome analysis is appropriate.

-If this test is ordered and the laboratory is informed that the patient is not on a COG protocol, this test will be canceled and automatically reordered by the laboratory as BALLF / B-Lymphoblastic Leukemia/Lymphoma, FISH, Varies.

Method Name

Fluorescence In Situ Hybridization (FISH)

Reporting Name

COG, ALL (B-cell), FISH

Specimen Type

Varies

Specimen Minimum Volume

Blood: 2 mL
Bone Marrow: 1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Clinical Information

In the United States the incidence of acute lymphoblastic leukemia (ALL) is roughly 6,000 new cases per year (as of 2009), or approximately 1 in 50,000. ALL accounts for approximately 70% of all childhood leukemia cases (ages 0-19 years), making it the most common type of childhood cancer. Approximately 85% of pediatric cases of ALL are B-cell lineage (B-ALL) and 15% are T-cell lineage (T-ALL). It has a peak incidence at 2 to 5 years of age. The incidence decreases with increasing age, before increasing again at around 50 years of age. ALL is slightly more common in males than females. There is an increased incidence of ALL in individuals with Down syndrome, Fanconi anemia, Bloom syndrome, ataxia telangiectasia, X-linked agammaglobulinemia, and severe combined immunodeficiency. The overall cure rate for ALL in children is about 90% and about 45% to 60% of adults have long-term disease-free survival. CRLF2/IGH rearrangements are more commonly observed in patients with Down syndrome or of Hispanic descent.

 

Specific genetic abnormalities are identified in the majority of cases of B-ALL, either by conventional chromosome studies or FISH studies. For more than 25 years, the Mayo Clinic Genomics Laboratory has served as a Children’s Oncology Group (COG) accredited laboratory for the performance of cytogenetic testing in pediatric patients being considered for enrollment in COG clinical trials and research. The laboratory is highly equipped to perform the time sensitive and critical cytogenetic testing necessary to assign risk stratification and facilitate enrollment in COG protocols.

 

Each of the B-ALL genetic subgroups are important to detect and can be critical prognostic markers. The decision for early transplantation may be made if t(9;22)(q34;q11.2), MLL (KMT2A) translocations, RUNX1 duplication/amplification or a hypodiploid clone is identified. In contrast, if ETV6/RUNX1 fusion is detected by FISH or hyperdiploidy is identified by chromosome studies, the patient has a favorable prognosis and transplantation is rarely considered.

 

A newly recognized World Health Organization (WHO) entity BCR-ABL1-like ALL, also known as Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL), is increasing in importance due to the poor prognosis seen in pediatric, adolescent, and young adult ALL. Common features of this entity involve rearrangements with tyrosine kinase genes involving the following genes: ABL2, PDGFRB, JAK2, ABL1, CRLF2, and P2RY8. Patients that have failed on conventional therapies have demonstrated favorable responses to targeted therapies when rearrangements involving these specific gene regions have been identified.

 

Evaluation of the MYC gene region is included in all diagnostic B-ALL panels to evaluate for Burkitt lymphoma. If a positive result is obtained, additional testing for the BCL2 and BCL6 gene regions may be considered.

 

Metaphase FISH confirmation of classic translocations that are cryptic and not visually detectable by chromosome analysis (ie, t[12;21] associated with ETV6/RUNX1 fusion) is performed as required by COG and is included as part of the electronic case submission by the Mayo Clinic Genomics Laboratory to COG for central review.

 

Additional cytogenetic techniques such as chromosomal microarray (CMAH / Chromosomal Microarray, Hematologic Disorders, Varies) may be helpful to resolve questions related to ploidy (hyperdiploid clone vs doubled hypodiploid clone) or to resolve certain clonal structural rearrangements such as the presence or absence of intrachromosomal amplification of chromosome 21 (iAMP21). Occasionally, characterization of balanced or complex rearrangements presumed to involve critical genes (such as a kinase activating gene and a fusion partner) may be characterizable by Mate Pair sequencing (MTRBM / MatePair, Targeted Rearrangements, Hematologic, Varies); a clinically validated next-generation sequencing technique developed at Mayo Clinic. A summary of the characteristic chromosome abnormalities identified in B-ALL is listed in the following table.

 

Common Chromosome Abnormalities in B-Acute Lymphoblastic Leukemia

Leukemia Type

Cytogenetic change

Typical demographic

Risk category

B-Acute Lymphoblastic Leukemia

t(12;21)(p13;q22), ETV6(TEL)/RUNX1(AML1)

Pediatric

Favorable

Hyperdiploidy

Pediatric

Favorable

t(1;19)(q23;p13.3), PBX1/TCF3

Pediatric

Intermediate

t(9;22)(q34;q11.2), BCR/ABL1

Pediatric/Adult

Unfavorable

iAMP21, RUNX1

Pediatric

Unfavorable

del(9p), CDKN2A(p16)

All ages

Variable

t(11q23;var), MLL

All ages

Unfavorable

t(4;11)(q21;q23), AFF1(AF4)/MLL

All ages

Unfavorable

t(6 ;11)(q27;q23), MLLT4/MLL

All ages

Unfavorable

t(9;11)(p22;q23), MLLT3(AF9)/MLL

All ages

Unfavorable

t(10;11)(p12;q23), MLLT10/MLL

All ages

Unfavorable

t(11;19)(q23;p13.1), MLL/ELL

All ages

Unfavorable

t(11;19)(q23;p13.3), MLL/MLLT1(ENL)

All ages

Unfavorable

t(14q32;var), IGH

All ages

Variable

t(X;14)(p22;q32)/t(Y;14)(p11;q32), CRLF2/IGH

Adolescent/Young Adult

Unfavorable

t(Xp22.33;var) or t(Yp11.32;var), CRLF2

All ages

Unfavorable

t(Xp22.3;var) or t(Yp11.32;var), P2RY8

All ages

Unfavorable

del(17p), TP53

All ages

Unfavorable

t(8q24.1;var), MYC

Pediatric/ Adolescent/

Young Adult

 

Complex karyotype (≥4 abnormalities)

Adult

Unfavorable

Low hypodiploidy/near triploidy

Adult

Unfavorable

Near-haploid/hypodiploid

All ages

Unfavorable

Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL)

t(1q25;var), ABL2

Pediatric/ Adolescent/

Young Adult

High Risk

 

 

 

 

t(5q33;var), PDGFRB

t(9p24.1;var), JAK2

t(9q34;var), ABL1

t(Xp22.33;var) or t(Yp11.32;var), CRLF2

t(Xp22.33;var) or t(Yp11.32;var), P2RY8

 

Reference Values

An interpretive report will be provided.

Interpretation

A neoplastic clone is detected when the percent of cells with an abnormality exceeds the normal reference range for any given probe.

 

The absence of an abnormal clone does not rule out the presence of a neoplastic disorder.

Clinical Reference

1. Moorman AV, Harrison CJ, Buck GA, et al: Karyotype is an independent prognostic factor in adult acute lymphoblastic leukemia (ALL): analysis of cytogenetic data from patients treated on the Medical Research Council (MRC) UKALLXII/Eastern Cooperative Oncology Group (ECOG) 2993 trial. Blood 2007 Apr 15;109(8):3189-3197

2. Moorman AV: The clinical relevance of chromosomal and genetic abnormalities in B-cell precursor acute lymphoblastic leukemia. Blood Rev 2012;26:123-135

3. Roberts KG, Li Y, Payne-Turner D, et al: Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med 2014 Sept;371(11):1005-1015

4. Mullighan CG: The genomic landscape of acute lymphoblastic leukemia in children and young adults. Hematology Am Soc Hematol Educ Program 2014 Dec 5;2014(1):174-180

5. Swerdlow SH, Campo E, Harris NL, et al: International Agency for Research on Cancer (IARC): World Health Organization (WHO) classification of tumours of haematopoietic and lymphoid tissues. IARC Press, Oxford University Press, 2017

Day(s) and Time(s) Performed

Specimens are processed Monday through Sunday.

Results reported Monday through Friday, 8 a.m.-5 p.m.

Analytic Time

7 days

Test Classification

This test was developed using an analyte specific reagent. Its performance characteristics were determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

88271 x 2, 88291-DNA probe, each (first probe set), Interpretation and report

88271 x 2-DNA probe, each; each additional probe set (if appropriate)

88271-DNA probe, each; coverage for sets containing 3 probes (if appropriate)

88271 x 2-DNA probe, each; coverage for sets containing 4 probes (if appropriate)

88271 x 3-DNA probe, each; coverage for sets containing 5 probes (if appropriate)

88274 w/modifier 52-Interphase in situ hybridization, <25 cells, each probe set (if appropriate)

88274-Interphase in situ hybridization, 25 to 99 cells, each probe set (if appropriate)

88275-Interphase in situ hybridization, 100 to 300 cells, each probe set (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
COGBF COG, ALL (B-cell), FISH In Process

 

Result ID Test Result Name Result LOINC Value
602296 Result Summary 50397-9
602297 Interpretation 69965-2
602298 Result Table 93356-4
602299 Result 62356-1
GC019 Reason for Referral 42349-1
GC020 Specimen 31208-2
602301 Source 31208-2
602302 Method 85069-3
602303 Additional Information 48767-8
602304 Disclaimer 62364-5
602305 Released By 18771-6